Fly Body Parts GO Data

library(R.filesets)

## Loading required package: R.oo

## Loading required package: R.methodsS3

## R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.

## R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.

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## Attaching package: 'R.oo'

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## R.filesets v2.15.0 (2022-07-21 10:00:05 UTC) successfully loaded. See ?R.filesets for help.

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## Attaching package: 'R.filesets'

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library(rrvgo)

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library(plotly)

## Loading required package: ggplot2

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## Attaching package: 'plotly'

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GO.info = read.csv("/Users/johncsantiago/Documents/GOcat_info.csv", row.names = 1)

GO.sim = function(GO.file){
  GO.data = GO.file[GO.file[,"p.adjust"]<.05,]
  GO.ontology = "BP"
  GO.use = row.names(GO.info)[GO.info$ontology == GO.ontology]
  GO.data = GO.data[intersect(row.names(GO.data), GO.use),]

  go_analysis = row.names(GO.data)

  scores = setNames(-log10(GO.data[,"p.adjust"]), go_analysis)

  simMatrix <- calculateSimMatrix(go_analysis,
                                orgdb="org.Dm.eg.db",
                                ont=GO.ontology,
                                method="Rel")
  return(simMatrix)
}
  
GO.rt = function(GO.file){
  GO.data = GO.file[GO.file[,"p.adjust"]<.05,]
  GO.ontology = "BP"
  GO.use = row.names(GO.info)[GO.info$ontology == GO.ontology]
  GO.data = GO.data[intersect(row.names(GO.data), GO.use),]

  go_analysis = row.names(GO.data)

  scores = setNames(-log10(GO.data[,"p.adjust"]), go_analysis)
  
  go_analysis = row.names(GO.data)

  reducedTerms <- reduceSimMatrix(simMatrix,
                                scores,
                                threshold=0.7,
                                orgdb="org.Dm.eg.db")

  return(reducedTerms)

}

##Head

GO.file = loadRDS("/Users/johncsantiago/Downloads/GO_Head_df")

simMatrix = GO.sim(GO.file)

## Loading required package: DOSE

## DOSE v3.24.2  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
## 
## If you use DOSE in published research, please cite:
## Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

## 

## preparing gene to GO mapping data...

## preparing IC data...

reducedTerms = GO.rt(GO.file)

##Thorax

GO.file = loadRDS("/Users/johncsantiago/Downloads/GO_Thorax_df")

simMatrix = GO.sim(GO.file)

## preparing gene to GO mapping data...

## preparing IC data...

reducedTerms = GO.rt(GO.file)

##Abdomen

GO.file = loadRDS("/Users/johncsantiago/Downloads/GO_Abdomen_df")

simMatrix = GO.sim(GO.file)

## preparing gene to GO mapping data...

## preparing IC data...

reducedTerms = GO.rt(GO.file)